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Given 3D MRI scans A, B, and C I want to perform an affine (co)registration of B onto A, take the transformation affine matrix of the registration and apply it on C.

My problem is that the affine matrix of the registration transform has the wrong signs. Maybe due to wrong orientation?

The TransformParameters contain 12 values of which the first 9 are the rotation matrix in row-major order and the last 3 are the translation values.

I'm annotating CT scan slices(Nifti format) with ITK-snap. One slice contains two labels(Subarachnoid and Intraparenchymal) in the same area. Here is the original annotated image link: https://ibb.co/FJpyVZF Since two labels are overlapping, the intersection area in the slice should contain both labels. But it shows it only contains the label which has been drawn last. Since the Subarachnoid area was drawn last over the Intraparenchymal area, the final segmented image only shows it contains Subarachnoid in the intersection region. I'm attaching the annotated slice https://ibb.co/F3TrXtq and segmented slice https://ibb.co/sRgdndY to clear my point. What can I do to make the intersection area contain two labels?

I am currently inheriting old code and trying to run it. As part of this there is an image generation done through ITK (which has been built and installed on the system)

The (truncated) function causing issue at the moment is the following

Using the example given on the itk website, I am able to get the RegularStepGradientDescentOptimizerv4 to work with MeanSquaresImageToImageMetricv4 and ImageRegistrationMethodv4 in python. However, when I want to use QuasiNewtonOptimizerv4, I get the error TypeError: in method 'itkImageRegistrationMethodv4REGv4F2F2_SetOptimizer', argument 2 of type 'itkObjectToObjectOptimizerBaseTemplateD *'.

My code for each is as follows.

ANTs open source provides transform functions that can move(frequently referred as normalizing or registration in neuroscience) one's brain MR image to other's brain MR image. But I got an error below : not all MR images but some MR images make below error. There NEVER exist any differences when I opened those MR images with image viewer like ITK-snap. It seems centain MR images that occurs those error must have mathematical or algebraic differences with images that does not occur error. How can I find out what the problem is?

Error message:

/opt/ANTs/bin/antsRegistrationSyNQuick.sh: line 464:

[[: _MR.nii: syntax error: invalid arithmetic operator (error token is ".nii")

antsRegistration call:

Crash happens in runtime on vtkSmartVolumeMapper::New() step. And it goes deep to vtkFixedPointVolumeRayCastMapper constructor. Don't understand how to tackle such an issue, please help

Exception thrown at 0x00007FF73A60735A in smop-ptqt.exe: 0xC0000005: Access violation reading location 0x0000000000000000.

Qt 5.15.6, VTK 9.1.0, ITK 5.2.1

I'm trying to convert the output of this code into a dataframe. The code takes a tab-separated txt file from AWS S3 and turns it into a csv

My problem is a bit wired. I am working on Prostate MRI dataset which contains dicom images. When I load dicom files using Simple ITK the output numpy array's dtype will be float64 . But when I load same dicom files using pydicom , the output numpy array's dtype will be uint16 And the problem isn't just this. Pixel intensities would be different when using different module. So my question is why they look different and which one is correct and why these modules load data differently? this is the code I'm using to load dcm files.

I have RGB images which I'm loading as a numpy array. I would like to convert these images into the nifty format, which I can open using ITK-SNAP (http://www.itksnap.org/pmwiki/pmwiki.php).

Here is what I have tried to do: